Atlantic salmon populations invaded by farmed escapees: quantifying genetic introgression with a Bayesian approach and SNPs (original) (raw)
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Aquaculture Environment Interactions, 2015
Farmed escapees may threaten the genetic integrity of native salmon populations through interbreeding. However, introgression requires survival until maturation, successful reproduction and successful early development. These traits are often compromised in domesticated animals selected for high performance in captivity. This makes it difficult to predict introgression levels in native populations. A recent study estimated genetic introgression of farmed escaped Atlantic salmon Salmo salar in 20 Norwegian rivers and found highly population-specific levels of introgression. The underlying causes of these patterns, however, remain unknown. Here, using a modeling approach on empirical and demographic data, we demonstrated that a combination of the observed relative frequency of escaped farmed salmon and the average annual angling catch weights for rivers, provides a significantly better predictor for cumulative introgression of farmed salmon in wild populations than the frequency of farmed salmon alone. Our results suggest that the demography of the native population is a significant factor influencing the relative success of farmed salmon in the wild.
Evolutionary Applications, 2021
domesticated animals alters the gene pool of wild populations and may constrain their viability and evolutionary potential (Glover et al., 2017; Naylor et al., 2005). Farmed domesticated animals are adapted to a captive environment and selected for characteristics that are of commercial importance. The same characteristics may reduce survival and reproductive success in the natural environment (Araki et al., 2007; Bertolotti et al., 2020). Domesticated animals may also originate from a limited set of founder populations and from a geographical range that does not reflect the genetic diversity of the species (Hindar et al., 1991). Reduced genetic diversity and nonnative origin are also commonly found in captive-bred animals that
Heredity, 2011
In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions.
PLoS ONE, 2012
Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world's largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15-30 years. In order to study the potential genetic impact, we conducted a spatiotemporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970-2010. Based upon the analysis of 22 microsatellites, individual admixture, F ST and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P = 0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global F ST = 0.038) and contemporary data sets (global F ST = 0.030), although significantly reduced with time (P = 0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global F ST dropped from 0.058 to 0.039, P = 0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population.
Genetic evidence of farmed straying and introgression in Swedish wild salmon populations
Aquaculture Environment Interactions, 2021
Escaped farmed Atlantic salmon represent a well-documented and ongoing threat to wild conspecific populations. In Norway, the world-leading producer of farmed salmon, annual monitoring of straying and genetic introgression by farmed escapees in wild salmon rivers has been carried out since the late 1980s. In this study, we applied molecular and statistical methods routinely used in the Norwegian monitoring programme to investigate the magnitude of escaped farmed salmon and genetic introgression in salmon rivers on the west coast of Sweden, where suspected escapees have been observed. Our results confirm that escaped farmed salmon stray, successfully spawn, and produce offspring at levels similar to those observed in neighbouring Norway. These findings raise concerns over population productivity and long-term viability and highlight the need for more permanent monitoring of the presence and consequences of escaped farmed salmon in Swedish salmon rivers. Our results further illustrate...
2011
Denne rapporten gjennomfører en kritisk gjennomgang av dagens kunnskap om interaksjoner mellom oppdrettslaks og ville laksepopulasjoner med spesifikk relevans for Norge, samt diskuterer dagens kunnskap om effektiv forvaltning av ville bestander av denne arten. Rapporten beskriver i detalj informasjon om akvakulturproduksjon, livssyklus, utbredelse og populasjonsstruktur, genetiske interaksjoner og bevaring av atlantisk laks. Et eget kapittel drøfter hvilke forskningsområder som trenger spesiell oppmerksomhet i tiden fremover.
PLoS ONE, 2013
The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960's for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964-1982) with frequencies in contemporary samples (2008-2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations.
Fish and Fisheries, 2017
Atlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentially locally adapted. Farmed salmon represent a limited number of wild source populations that have been exposed to ≥12 generations of domestication. Consequently, farmed and wild salmon differ in many traits including molecular-genetic polymorphisms, growth, morphology, life history, behaviour, physiology and gene transcription. Field experiments have demonstrated that the offspring of farmed salmon display lower lifetime fitness in the wild than wild salmon and that following introgression, there is a reduced production of genetically wild salmon and, potentially, of total salmon production. It is a formidable task to estimate introgression of farmed salmon in wild populations where they are not exotic. New methods have revealed introgression in half of ~150 Norwegian populations, with point estimates as high as 47%, and an unweighted average of 6.4% across 109 populations. Outside Norway, introgression remains unquantified, and in all regions, biological changes and the mechanisms driving population-specific impacts remain poorly documented. Nevertheless, existing knowledge shows that the long-term consequences of introgression is expected to lead to changes in life-history traits, reduced population productivity and decreased resilience to future challenges. Only a major reduction in the number of escapees and/or sterility of farmed salmon can eliminate further impacts.
Model-based evaluation of the genetic impacts of farm-escaped Atlantic salmon on wild populations
Aquaculture Environment Interactions, 2019
Genetic interactions (i.e. hybridization) between wild and escaped Atlantic salmon Salmo salar from aquaculture operations have been widely documented, yet the ability to incorporate predictions of risk into aquaculture siting advice has been limited. Here we demonstrate a model-based approach to assessing these potential genetic interactions using a salmon aquaculture expansion scenario in southern Newfoundland as an example. We use an eco-genetic individual-based Atlantic salmon model (IBSEM) parameterized for southern Newfoundland populations, with regional environmental data and field-based estimates of survival, to explore how the proportion of escapees relative to the size of wild populations could potentially influence genetic and demographic changes in wild populations. Our simulations suggest that both demographic decline and genetic change are predicted when the percentage of escapees in a river relative to wild population size is equal to or exceeds 10% annually. The occu...